The Mysteries of Evolution: 2. The Origin of Life and the miserable failure to reassemble Humpty Dumpty

Not much can be written after you watch the two videos above…

It is pretty easy to understand for those who choose to understand that the theory of abiogenesis and the probability of life spontaneously self-assembling is just a science-fiction story to fill the void for those who need to believe in something other than the obvious…

If the living cell can’t be reassembled in a lab, what evidence is there that life spontaneously self-assembled other than in science-fiction stories?

Now, let’s listen to the excuses…

192 thoughts on “The Mysteries of Evolution: 2. The Origin of Life and the miserable failure to reassemble Humpty Dumpty”

  1. CharlieMCharlieM

    OMagain: I’ll take that as ‘no’ then.

    I’m not sure why you are so interested in their beliefs. Do you think that the opinion of the majority should be regarded as the correct opinion?

  2. OMagain

    CharlieM: I’m not sure why you are so interested in their beliefs. Do you think that the opinion of the majority should be regarded as the correct opinion?

    I’m simply pointing out the asymmetry here. Their work supports your ideas you say, but they would not agree with your ideas in turn, which you’ve now labeled a belief. And interesting that “belief” now comes into it. Do you think their scientific work was in any way influenced by their beliefs? Is yours?

  3. MungMung

    CharlieM: I’m not sure why you are so interested in their beliefs. Do you think that the opinion of the majority should be regarded as the correct opinion?

    I think we should vote on that.

  4. CharlieMCharlieM

    OMagain: I’m simply pointing out the asymmetry here. Their work supports your ideas you say, but they would not agree with your ideas in turn, which you’ve now labeled a belief. And interesting that “belief” now comes into it. Do you think their scientific work was in any way influenced by their beliefs? Is yours?

    Their work supports my worldview only in the facts that they bring to light. The work they are doing will uncover facts irrespective of their worldview, or my worldview, or of anyone’s worldview. And those facts point to there being a consciousness which is not limited to individual organisms but comes from the workings of the group as a whole.

    According to this article, “In Newly Created Life-Form, a Major Mystery”, in Quantamagazine, Craig Ventner’s team produced a tiny organism named syn3.0 that contains just 473 genes. This article is worth reading (or alternatively there is an attached audio of it).

    They say they have produced a viable organism containing 473 genes. They can say that this is a fact only because they have done the work. I, on the other hand, have to take it on faith that they have actually done this. I can say that I really believe they have done this, but unless I was there or repeated their work myself then all I can say is that it is my belief that they have done this. Much of the work done in the name of science has to be taken on faith by the general public and even by other scientists because of the specialist nature of research .these days. We cannot claim as a guaranteed fact that which we have not witnessed.

    From the article:

    Venter’s minimal cell is a product not just of its environment, but of the entirety of the history of life on Earth. Sometime in biology’s 4-billion-year record, cells much simpler than this one must have existed. “We didn’t go from nothing to a cell with 400 genes,” Szostak said. He and others are trying to make more basic life-forms that are representative of these earlier stages of evolution.

    Jack Szostak’s statement is not a statement of fact but one of belief. No one knows how the first life began but he confidently asserts that it did not begin with a cell of 400 genes suddenly appearing. By stating this he is going beyond the facts and he does this because of his prior belief in a naturalist view of how life came about on earth.

  5. CharlieMCharlieM

    OMagain: Do you think their scientific work was in any way influenced by their beliefs? Is yours?

    It would be naive to think otherwise in either case.

  6. colewd

    CharlieM,

    Jack Szostak’s statement is not a statement of fact but one of belief. No one knows how the first life began but he confidently asserts that it did not begin with a cell of 400 genes suddenly appearing. By stating this he is going beyond the facts and he does this because of his prior belief in a naturalist view of how life came about on earth.

    Exactly. Another assumption is that a eukaryotic cell comes from earlier precursors yet its contents and architecture are very unique. There is a clear mis match between the evidence and the simple to complex theory.

  7. CharlieMCharlieM

    From the article I linked to above:

    Yet within those 473 genes lies a gaping hole. Scientists have little idea what roughly a third of them do. Rather than illuminating the essential components of life, syn3.0 has revealed how much we have left to learn about the very basics of biology.

    “To me, the most interesting thing is what it tells us about what we don’t know,” said Jack Szostak, a biochemist at Harvard University who was not involved in the study. “So many genes of unknown function seem to be essential.”

    “We were totally surprised and shocked,” said Venter, a biologist who heads the J. Craig Venter Institute in La Jolla, Calif., and Rockville, Md., and is most famous for his role in mapping the human genome. The researchers had expected some number of unknown genes in the mix, perhaps totaling five to 10 percent of the genome. “But this is truly a stunning number,” he said.

    It continues:

    But it is unclear what the remaining 149 genes do. Scientists can broadly classify 70 of them based on the genes’ structure, but the researchers have little idea of what precise role the genes play in the cell. The function of 79 genes is a complete mystery. “We don’t know what they provide or why they are essential for life — maybe they are doing something more subtle, something obviously not appreciated yet in biology,” Venter said. “It’s a very humbling set of experiments

    Venter’s team is eager to figure out what the mystery genes do, but the challenge is multiplied by the fact that these genes don’t resemble any other known genes..”

    And it is not as though these genes are the common starting point for evolution. As Venter says, “If he had done the same set of experiments with a different microbe, he points out, he would have ended up with a different set of genes.”

    We may want to think about what this means for the belief in common descent from a single source?

  8. newton

    CharlieM: Jack Szostak’s statement is not a statement of fact but one of belief. No one knows how the first life began but he confidently asserts that it did not begin with a cell of 400 genes suddenly appearing. By stating this he is going beyond the facts and he does this because of his prior belief in a naturalist view of how life came about on earth.

    It is based on an assumption of naturalism as a practical choice, for a cell to appear fully formed would require another assumption of what and when and how the designer did what he did.. One assumption lends itself to further study ,the other has not so much.

  9. GlenDavidson

    CharlieM: Jack Szostak’s statement is not a statement of fact but one of belief. No one knows how the first life began but he confidently asserts that it did not begin with a cell of 400 genes suddenly appearing. By stating this he is going beyond the facts and he does this because of his prior belief in a naturalist view of how life came about on earth.

    Or, you know, because he’s not going to invoke causes for which there is no evidence, like some people do.

    Likewise with ball lightning, legitimate scientists look for “naturalistic explanations” because they don’t just make things up.

    Glen Davidson

  10. GlenDavidson

    colewd:
    CharlieM,

    Exactly.Another assumption is that a eukaryotic cell comes from earlier precursors yet its contents and architecture are very unique.

    Maybe you’d like to explain the continuity between prokaryotes and eukaryotes, as well as the differences. You know, the kind of evidence you’d expect from evolution. But then, you don’t explain, you just try to knock down real explanations.

    There is a clear mis match between the evidence and the simple to complex theory.

    Yeah right, eukaryotes appear a billion or more years after prokaryotes, and you think there’s a mismatch. I wouldn’t expect you to care about the more complex appearing rather later than simpler organisms, but people who want actual explanation do.

    Glen Davidson

  11. Fair WitnessFair Witness

    CharlieM: ….As Venter says, “If he had done the same set of experiments with a different microbe, he points out, he would have ended up with a different set of genes.”

    We may want to think about what this means for the belief in common descent from a single source?

    It means that microbes have been around a while and the genomes of different microbes have diverged from one another.

  12. RumraketRumraket

    CharlieM: Jack Szostak’s statement is not a statement of fact but one of belief. No one knows how the first life began but he confidently asserts that it did not begin with a cell of 400 genes suddenly appearing. By stating this he is going beyond the facts and he does this because of his prior belief in a naturalist view of how life came about on earth.

    No, I’m sorry but this is simply false.

    We don’t need to know how exactly life began to have good rational and evidential reasons for believing it did not spring into existence in the form of a relatively complex modern cell. From the standpoint of probability alone, it is more reasonable to believe that a simpler thing can form spontaneously than it is that a complex thing will. Or stated another way, it is more likely that a simpler thing will form, than it is that a more complex thing will form. Whether you espous metaphysical naturalism or not.

    Besides, there is actually evidence for stages of life where organisms were simpler than the putative last universal common ancestor. Traces of these stages are seen, for example, in the components of the translation system. Did you know that fragments of sequences encoding tRNA molecules for all 20 canonical amino acids, RNA polymerases, DNA polymerases, ribosomal proteins and various metabolic enzymes can still today be found in ribosomal RNA sequence? They’re no longer functional genes which are transcribed into product. But they exist and are identifiably there, in ribosomal RNA sequence, nevertheless.
    See this and this.

    The two classes of aminoacyl-tRNA-synthetases all derive from two common ancestral protein coding genes. The DNA/RNA sequences of these genes, when analyzed, are basically the two anti-parallel strands of the same single gene. Isn’t that curious?

    There’s more like this. These are all hints of a simpler stage of life. Someone like you would have to explain why we still find these curious fragments in extant life if there was never actually a simpler stage of life when these components were in use.

  13. colewd

    newton,

    It is based on an assumption of naturalism as a practical choice, for a cell to appear fully formed would require another assumption of what and when and how the designer did what he did.. One assumption lends itself to further study ,the other has not so much.

    When the evidence points against a natural explanation yet you pursue one what are you doing except wasting valuable resources.

    How many dead ends do you have to reach in the name of materialism to finally reach the conclusion that it is a faulty assumption with most the evidence pointing in another direction of complexity suddenly appearing.

    Szostak is trying to pursue origin of life based on his simple to complex assumption. Venter is pursuing building a proto cell and is doing experimental biology without materialistic assumptions. Who is adding the most value to scientific understanding? Are Szostak’s assumptions adding value?

  14. OMagain

    colewd: When the evidence points against a natural explanation yet you pursue one what are you doing except wasting valuable resources.

    What evidence?

    colewd: How many dead ends do you have to reach in the name of materialism to finally reach the conclusion that it is a faulty assumption with most the evidence pointing in another direction of complexity suddenly appearing.

    All of them, silly. How do you know it’s a dead end till you get to the end?

  15. OMagain

    colewd,
    Can you give a single example where the search for a natural explanation was abandoned in favor of a (presumably) immaterial explanation?

    A single example?

  16. RumraketRumraket

    colewd: Venter is pursuing building a proto cell and is doing experimental biology without materialistic assumptions.

    No, venter isn’t building a protocell. A protocell is the name for a hypothetical first cell that existed after the origin of life. His work has nothing to do with the origin of life. Venter is trying to create a synthetic cell, not a protocell.

    And Craig Venter is using the same basic assumptions as they do in the Szostak lab: Living cells are made of atoms and molecules acted on by the laws of physics and chemistry and nothing else.

    As usual you have no idea what you’re talking about.

    Who is adding the most value to scientific understanding? Are Szostak’s assumptions adding value?

    Assumptions themselves don’t “add value”, they guide your research. Not that it even matters who adds the “most” value to scientific understanding. Supposing either of them adds “more” value than the other, does that make the other one’s work worthless or not worth it? No, it doesn’t.

    Just like Venters, Szostak’s work has implications for lots of molecular biology and biophysics (since his lab does lots of work on membrane biophysics and the mechanics of RNA and DNA replication, including sythetic polymers).

    The fact that you personally don’t like Szostak’s work has no bearing on what the impact of it is or will be in the future. And you are painfully clueless about what even goes on in that lab (and curiously, in Venters too).

  17. OMagain

    colewd: Venter is pursuing building a proto cell and is doing experimental biology without materialistic assumptions.

    Citation please! I’m interested to hear more….

  18. colewd

    OMagain,

    What evidence?

    The eukaryotic cell with no evidence of precursors to the spliceosome, the nuclear pore complex, the golgi apparatus, chromosome structure etc.

    Multicellular life with no precursors to the explosion to the multicellular Cambrian animals.

    Sudden appearance of fully formed structures in the fossil records.

    All of them, silly. How do you know it’s a dead end till you get to the end?

    We need to make choices where to spend resources based on potential success. How much time have we spent on OOL research? What have we demonstrated?

  19. colewd

    colewd,

    Assumptions themselves don’t “add value”, they guide your research. Not that it even matters who adds the “most” value to scientific understanding. Supposing either of them adds “more” value than the other, does that make the other one’s work worthless or not worth it? No, it doesn’t.

    Money drives research. You need to make choices so value will eventually win the day.

  20. RumraketRumraket

    colewd:
    OMagain,

    The eukaryotic cell with no evidence of precursors to the spliceosome, the nuclear pore complex, the golgi apparatus, chromosome structure etc.

    I’m guessing you’ve done literally zero work searching for homologous structures or homologues of the proteins involved.

    Multicellular life with no precursors to the explosion to the multicellular Cambrian animals.

    Another creationist outright falsehood.

    Sudden appearance of fully formed structures in the fossil records.

    What the hell else should they be, half-formed?

    We need to make choices where to spend resources based on potential success.

    Then all IDcreationist institutions should be dismantled and closed immediately.

    How much time have we spent on OOL research?

    In comparison with so many other projects, a neglible amount. There’s a handful of labs in the world directly conducting experiments related to the origin of life and they’ve been going for a couple of decades at most.

    What have we demonstrated?

    That list is long. We still don’t know how life originated, but that’s different from saying there has not been any progress. Progress is slow exactly because research in the origin of life is down-prioritized, extremely under-funded, and only very few people work on it. At best a few people do some work on it when they do their PhD for a short time, before they go on to more lucrative endeavours in medicine or private industry. It is notoriously hard to make a living having the origin of life as your primary research interest, and anyone who works on it doesn’t work on that exclusively, but sort of do it on the side when they can secure funding for some experiment.
    The few labs who can manage to focus on it primarily do so because the scientists running those labs are already highly accomplished and somewhat famous (such as Jack Szostak who got a nobel prize). The only other exception I know to his is NASA where afaik a single group of people do work on the origin of life.

  21. OMagain

    colewd: Sudden appearance of fully formed structures in the fossil records.

    How are you using the word “sudden” there? Are we talking seconds? Minutes? Hours? Hundreds of millions of years?

  22. OMagain

    colewd: The eukaryotic cell with no evidence of precursors to the spliceosome, the nuclear pore complex, the golgi apparatus, chromosome structure etc.

    The mere existence of those things is evidence for their supernatural origin? Why?

  23. colewd

    OMagain,

    How are you using the word “sudden” there? Are we talking seconds? Minutes? Hours? Hundreds of millions of years?

    From a simple multicellular organism like a sponge to a Cambrian animal with a respiratory system, nervous system and muscular system I think any of the above time frames are sudden if you are talking about a trial and error process developing these complex systems.

  24. colewd

    OMagain,

    The mere existence of those things is evidence for their supernatural origin? Why?

    By supernatural do you mean beyond a material explanation?

  25. John HarshmanJohn Harshman

    colewd: From a simple multicellular organism like a sponge to a Cambrian animal with a respiratory system, nervous system and muscular system I think any of the above time frames are sudden if you are talking about a trial and error process developing these complex systems.

    And yet the fossil record seems to show such a thing happening. What exactly is complex about any of those systems? They seem simple enough to me. A nervous system is just a collection of nerve cells and synapses lined up, often with simple, direct connections between sensory neurons and muscles. A respiratory system can be as simple as skin through which oxygen can diffuse. And a muscular system can be as simple as just a collection of cells that all contract in synchrony.

    Anyway, where do you get your estimates for how long it takes for natural processes to develop such things?

  26. colewd

    John Harshman,

    And yet the fossil record seems to show such a thing happening. What exactly is complex about any of those systems? They seem simple enough to me. A nervous system is just a collection of nerve cells and synapses lined up, often with simple, direct connections between sensory neurons and muscles. A respiratory system can be as simple as skin through which oxygen can diffuse. And a muscular system can be as simple as just a collection of cells that all contract in synchrony.

    The challenge here is in the detail of how new DNA sequences were stumbled upon to create this very complex system (cells tissue etc) that needs to be complete to have viable function. We are taking a complex set of new DNA sequences that lead to cells, proteins and tissues which all have to work together to construct a viable animal. I do not believe this is possible without a plan that contains foresight. A step by step process is very unlikely to stumble upon all these new sequences.

  27. colewd

    John Harshman,

    This is Koonen’s paper which I have read.

    What is your purpose in mentioning it?

    Rumraket wanted to know if I had looked at proposed homologies between eukaryotic cells and prokaryotic and archaea cell types. This paper is a good review.

  28. Adapa

    colewd:
    .I do not believe this is possible without a plan that contains foresight.

    What you do not believe based on your ignorance and personal incredulity doesn’t matter to the scientific community.

    A step by step process is very unlikely to stumble upon all these new sequences.

    Why not? What evidence do you have these particular sequences are the only ones possible to sustain life?

  29. John HarshmanJohn Harshman

    colewd:
    John Harshman,

    The challenge here is in the detail of how new DNA sequences were stumbled upon to create this very complex system (cells tissue etc) that needs to be complete to have viable function.We are taking a complex set of new DNA sequences that lead to cells, proteins and tissues which all have to work together to construct a viable animal.I do not believe this is possible without a plan that contains foresight. A step by step process is very unlikely to stumble upon all these new sequences.

    Do you ever read what you’re replying to? Who says the system is necessarily very complex? Who says that new DNA sequences were needed in the early evolution of metazoans? It’s unlikely that more than the ordinary number (very few) of genes not present in earlier taxa were involved in early eumatazoan evolution. Why would you suppose otherwise?

    All you have is your personal incredulity; but try applying that incredulity to whatever highly complicated entity you think applied the “plan that contains foresight”. How does it hold up?

    Oh, and have you taken my hint and read my fairly recent post here, Jonathan Wells and the Cambrian Explosion? It might help deal with a few of your misunderstandings of that event, including your notion of “it has to be complete to have viable function”.

  30. MungMung

    John Harshman: Anyway, where do you get your estimates for how long it takes for natural processes to develop such things?

    Where’s yours? It’s your theory. I know, here’s an idea, let’s try to shift the burden of proof. Same old b.s.

  31. colewd

    John Harshman,

    Do you ever read what you’re replying to? Who says the system is necessarily very complex?

    So your claim here is that a multicellular organism with directed muscle movement by a central nervous system and a respiratory system can be built with simple changes to the DNA of a sponge?

    Oh, and have you taken my hint and read my fairly recent post here, Jonathan Wells and the Cambrian Explosion? It might help deal with a few of your misunderstandings of that event, including your notion of “it has to be complete to have viable function”.

    Yes, I have read it but you never address the complexity argument except to make the claim that you can build a complex animal with simple DNA changes. I think this is a claim based on underestimating the complexity required for functional multicellular biology (requiring respiratory systems and controlled muscle movement) and embryology.

    So why do you reject almost all of what it says?

    Have you read the paper? Do you think it supports a known evolutionary path to eukaryotic cells?

  32. colewd

    Mung,

    Where’s yours? It’s your theory. I know, here’s an idea, let’s try to shift the burden of proof. Same old b.s.

    The trend is the same for the materialists.
    OOL: LUCA must be simpler then what we see today.

    Origin of the eukaryotic cell; Their must have been something more complex then the prokaryotic cells that are now extinct.

    Origin of respirating and mobile multicellular organisms: The DNA must have been originally simpler.

    The evidence does not support the conclusion so a “just so” story evolves 🙂

  33. John HarshmanJohn Harshman

    colewd:
    John Harshman,

    So your claim here is that a multicellular organism with directed muscle movement by a central nervous system and a respiratory system can be built with simple changes to the DNA of a sponge?

    That’s what the genomic evidence would seem to indicate. And let’s remember that there are extant species with a great many intermediate sorts of morphologies.

    Yes, I have read it but you never address the complexity argument except to make the claim that you can build a complex animal with simple DNA changes.I think this is a claim based on underestimatingthe complexity required for functionalmulticellular biology (requiring respiratory systems and controlled muscle movement) and embryology.

    I think you have no idea what complexity is required. Your continued harping on respiratory systems is a case in point. Many animals have no respiratory system in particular besides a gas-permeable skin and body fluids around the tissues. Similarly, many animals have no brains, just nerve nets with simple connections.

    Have you read the paper?Do you think it supports a known evolutionary path to eukaryotic cells?

    Nope, haven’t read it. But you didn’t answer my question.

  34. John HarshmanJohn Harshman

    colewd: The evidence does not support the conclusion so a “just so” story evolves

    Bold words for a person who is unacquainted with the evidence and is unwilling to discuss it.

  35. RumraketRumraket

    colewd: DOI: 10.1186/gb-2010-11-5-209

    This is Koonen’s paper which I have read.

    Why are you reading a paper that uses the very same phylogenetic methods you normally always reject, to somehow argue that the last eukaryotic common ancestor was a relatively complex cell? You believe these methods don’t work and are “just so” stories. By extension, you must reject the conclusions of this paper. Alternatively, you may continue to be a hypocrite.

  36. RumraketRumraket

    colewd: The challenge here is in the detail of how new DNA sequences were stumbled upon to create this very complex system (cells tissue etc) that needs to be complete to have viable function. We are taking a complex set of new DNA sequences that lead to cells, proteins and tissues which all have to work together to construct a viable animal. I do not believe this is possible without a plan that contains foresight.

    Your personal belief is not itself an argument for anything.

    A step by step process is very unlikely to stumble upon all these new sequences.

    Please show your math.

  37. RumraketRumraket

    Mung: John Harshman: Anyway, where do you get your estimates for how long it takes for natural processes to develop such things?

    Where’s yours? It’s your theory. I know, here’s an idea, let’s try to shift the burden of proof. Same old b.s.

    From fossil chronologies and comparative genetic evidence (molecular clock estimates). Those are what tell us how long it took for these things to develop.

    Back to you… oh wait you had nothing and was trying to deflect. Check!

  38. RumraketRumraket

    colewd:
    Mung,

    The trend is the same for the materialists.
    OOL: LUCA must be simpler then what we see today.

    And there is evidence that it was. Yes, phylogenetic evidence. That thing you reject yet curiously cite when you (ironically) mistakenly think the results support your case.

    Origin of the eukaryotic cell; Their must have been something more complex then the prokaryotic cells that are now extinct.

    Again, there is evidence for this.

    First of all, the fact that prokaryotes exist and are simpler than eukaryotes shows it is most definitely possible for an organism simpler than any eukaryote to exist.

    Also, many structures and proteins used by eukaryotes are homologous to simpler versions of them that exist in prokaryotes. This is evidence. This is what evolutionary theory requires, but design can only explain in ad-hoc fashion.

    Origin of respirating and mobile multicellular organisms:The DNA must have been originally simpler.

    What does this even mean? “The dna must have been simpler”?

  39. CharlieMCharlieM

    newton: It is based on an assumption of naturalism as a practical choice, for a cell to appear fully formed would require another assumption of what and when and how the designer did what he did.. One assumption lends itself to further study ,the other has not so much.

    Note that the only person bringing a designer, and a male designer at that, into the conversation is you.

    If original physical cell did not just appear from nowhere but was the physical manifestation of the archetypal cell analogous to the way a crystal is a condensation of the material in solid form, then that is something which can certainly warrant further study.

  40. CharlieMCharlieM

    GlenDavidson: Or, you know, because he’s not going to invoke causes for which there is no evidence, like some people do.

    Likewise with ball lightning, legitimate scientists look for “naturalistic explanations” because they don’t just make things up.

    Glen Davidson

    Naturalistic explanations are fine so long as it is realised that they are only one level of explanation and they don’t preclude other ways of explanation. For example a boxing match could be described very accurately in terms of the physics and chemistry of muscle movements and damaged cells. There would be nothing false about this but it would tell us nothing about the actual people involved. Considering the people would involve explanations which have gone beyond the physics and chemistry into a higher realm.

  41. CharlieMCharlieM

    Fair Witness: It means that microbes have been around a while and the genomes of different microbes have diverged from one another.

    And that could be the case in either scenario, a single source or multiple sources.

  42. newton

    CharlieM: Naturalistic explanations are fine so long as it is realised that they are only one level of explanation and they don’t preclude other ways of explanation. For example a boxing match could be described very accurately in terms of the physics and chemistry of muscle movements and damaged cells. There would be nothing false about this but it would tell us nothing about the actual people involved. Considering the people would involve explanations which have gone beyond the physics and chemistry into a higher realm

    That is of course an assumption that human emotions and thoughts are not part of nature.

  43. RumraketRumraket

    CharlieM: There would be nothing false about this but it would tell us nothing about the actual people involved.

    You claim this, but it isn’t obvious why this would be the case. If you really actually could give a total description of a boxing match at the atomic level, why would this NOT tell us anything about the actual people involved?

    It seems to me the only thing that makes this practically infeasible is the fact that we as human beings don’t have sufficient cognitive resources to really imagine and hold in our minds eye, a boxing match taking place between such unfathomably vast numbers of particles. Combined with the inordinate amount of time and space such an account would take to relay or store somewhere.

    As such, it is not clear that a “materialist” account of a boxing match at the level of atoms is actually lacking any information about the participants (or which could not at least in princple be derived from such an accout), the fundamental barrier is the challenges set by the limits of human cognition.

  44. CharlieMCharlieM

    Rumraket,

    You are providing evidence for one scenario, others have argued for a different scenario, such as here

    The origin and evolution of the ribosome have been always mysterious and have prompted a multitude of hypotheses. Many origin scenarios continue to be inspired by the ancient RNA world theory (e.g. [108]; [109] ; [110]). These scenarios generally place the origin of the complex in its catalytic center. However, the ribosome holds several functional roles besides being a catalyst for the synthesis of peptide bonds ( Fig. 4A). The ribosome is also a gatekeeper, policing genetic code discrimination during decoding, and fundamentally, a turnstile capable of molecular mechanics and information and energy transfer. Which of these three general ribosomal roles in cells is uniquely universal, central and likely ancient? A cursory analysis provides preliminary clues:…

    What are the molecular evolution and origin-of-life implications of the reconstructed history of molecular accretion in proteomes and ribosomes? Phylogenomic data embedded in hundreds-to-thousands of proteomes provide strong support to an alternative model of origin of biochemistry, translation and early life that is different and has more explanatory power than the widely accepted ‘RNA world’ paradigm…

    However and remarkably, phylogenomic analysis reveals that interactions of polypeptides with nucleic acids materialized for the first time later than interactions with cofactors and membranes, suggesting that genetics and its associated molecular functions were late additions to the functional repertoire of primordial life

    These are competing theories, not facts.

    From one of your links

    The ribosome as a missing link in prebiotic evolution II: Ribosomes encode ribosomal proteins that bind to common regions of their own mRNAs and rRNAs.

    Since these ribosome-binding proteins (rb-proteins) must bind to the rRNA, but the rRNA also functioned as mRNA, it follows that rb-proteins should bind to their own mRNA as well. This hypothesis can be contrasted to a “null” hypothesis in which rb-proteins evolved independently of the rRNA sequences and therefore there should be no necessary similarity between the rRNA to which rb-proteins bind and the mRNA that encodes the rb-protein.

    I have a different proposal and that is that none of the components of the first cell was primal, the nucleic acids, the proteins, the membranes, they all evolved simultaneously.

  45. CharlieMCharlieM

    Rumraket: And Craig Venter is using the same basic assumptions as they do in the Szostak lab: Living cells are made of atoms and molecules acted on by the laws of physics and chemistry and nothing else…

    Just like Venters, Szostak’s work has implications for lots of molecular biology and biophysics (since his lab does lots of work on membrane biophysics and the mechanics of RNA and DNA replication, including sythetic polymers).

    From Stephen Talbott

    There is every variety and degree of atomic and molecular interaction, so that even classifying the types of molecular bonds has proven a perennial vexation for chemists and physicists. In an instructive essay called “Beyond the Bond”, Nature columnist Philip Ball (2011*), mentions how “the behaviour of one electron depends on what all the others are doing”. More than that, “describing the quantum chemical bond remains a matter of taste: all descriptions are, in effect, approximate ways of carving up the electron distributions”. Ball quotes Roald Hoffmann of Cornell University to the effect that “any rigorous definition of a chemical bond is bound to be impoverishing”. According to Ball, “the static picture of molecules with specific shapes and bond strengths” needs replacing, and we must learn to view “bonds as degrees of attraction that wax and wane …”

    The remarkable thing is how little this understanding has colored the rhetoric of biologists when they talk about molecular machines — for example, the RNA polymerase that transcribes DNA into RNA, the spliceosome that pieces together well-chosen snippets of a precursor messenger RNA (mRNA) into a mature form, and the ribosome that translates mRNAs into protein.

    It is well to realize that each of these supposed “machines” is a massive complex of continuously changing molecular composition, with the component molecules themselves subject to modifications crucial for their functioning. All these changes represent an unfathomably intricate shifting of chemical and physical bonds — a qualitative reconfiguring of the balance of forces. This mean that there is an ongoing, even if often subtle, transformation of substances — the kind of transformation that, at one extreme, produces water from hydrogen and oxygen and, at the other, alters the forces and energies within some portion of a macromolecule just enough to shift its biological activity from one pathway to another.

    Where is the justification for interpreting these biochemical metamorphoses as machine interactions?

    Mysteries of water. It is also emerging that the cellular contents manifest a kaleidoscopically changing pattern of locally distinct phases — liquid, semi-liquid, solid, gel, and so on. Working with flatworms, Hubstenberger et al. (2013*) found that as egg cells mature, many highly viscous, semi-liquid molecular complexes become more dynamic liquid droplets and their constituents become more mobile, which is thought to promote rapid changes in organization of the complexes after fertilization — changes, for example, that facilitate the differentiation of cells in the growing embryo. Again, where is the “machinery” in this?

  46. RumraketRumraket

    CharlieM: Rumraket,

    You are providing evidence for one scenario

    No, you mistake my intent here. I’m not arguing for some particular hypothesis for the origin of the translation system and the genetic code, rather I am arguing that there is evidence that indicates that they are evolved entities with an evolutionary history that goes back to a time before the last universal cellular ancestor.

    I did this specifically because Bill Cole usually declares with great conviction that there isn’t any evidence that life was ever simpler than studies that try to reconstruct the genomic content of the Last Universal Common Ancestor, imply.

    These are competing theories, not facts.

    I don’t disagree, none the various proposed hypotheses for the origin of the ribosome and the translation system are facts.

    Rather, what is a fact is that when we analyze the various components involved in translation, we see evidence that testifies that they themselves evolved. That they have an evolutionary history, and there was a simpler stage of life with functionally and structurally simpler, less complex versions of the things we seen in life today.

    I brought up the particular papers I did as examples detailing evidence for this latter view. For example, the evidence that ribosomal RNA genes*, once were part of the ribosomal RNA itself. In other words, that pieces of ribosomal RNA itself could be directly copied into an mRNA molecule which could be translated into protein.

    * (and many others, such as RNA and DNA polymerases, metabolic enzymes, tRNAs and so on, all of which today, in our very own genome, has their own separate genes).

    The ribosome as a missing link in prebiotic evolution II: Ribosomes encode ribosomal proteins that bind to common regions of their own mRNAs and rRNAs.

    Since these ribosome-binding proteins (rb-proteins) must bind to the rRNA, but the rRNA also functioned as mRNA, it follows that rb-proteins should bind to their own mRNA as well. This hypothesis can be contrasted to a “null” hypothesis in which rb-proteins evolved independently of the rRNA sequences and therefore there should be no necessary similarity between the rRNA to which rb-proteins bind and the mRNA that encodes the rb-protein.

    I have a different proposal and that is that none of the components of the first cell was primal, the nucleic acids, the proteins, the membranes, they all evolved simultaneously.

    I think you misunderstood what you quoted. The statement they make there isn’t actually incompatible with what you just suggested.

    They are not advocating for a particular chronology of RNA vs protein (that either came before the other). Rather, they are specifically addressing the genomic organization (in particular, was mRNA and rRNA distinct and separate genes in the primeval organism?) of whatever organism in which the ribosomal proteins evolved. Were the analyzed ribosomal proteins first encoded in their own genes that were located elsewhere in the genome, or were they encoded directly in ribosomal RNA sequence itself? They are arguing that ribosomal RNA itself originally included the genes encoding ribosomal protein. Not that either came before the other.

    I think you have mistaken both mine and the author’s intentions. Neither of us are advocating for some sort of pure RNA world to precede peptides and proteins.

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